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Commit c201391e authored by Julien Cornut's avatar Julien Cornut
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%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
# This lib is needed to parse fastq easily # This lib is needed to parse fastq easily
from Bio import SeqIO from Bio import SeqIO
# This lib is used to avoid using a bash magic cell to copy a file # This lib is used to avoid using a bash magic cell to copy a file
from shutil import copyfile from shutil import copyfile
# Used to... list directory # Used to... list directory
from os import listdir, path from os import listdir, path
# Check the time taken by a function to run # Check the time taken by a function to run
import datetime import datetime
# Enter/Uncomment here the name of the file you want to process # Enter/Uncomment here the name of the file you want to process
# fname = "Undetermined_lane7_pair1" # fname = "Undetermined_lane7_pair1"
# fname = "flowcell261_lane8_pair1_CAGATC" # fname = "flowcell261_lane8_pair1_CAGATC"
# fname = "flowcell261_lane8_pair1_TGACCA" # fname = "flowcell261_lane8_pair1_TGACCA"
# fname = "flowcell362_lane4_pair1_ACAGTG" # fname = "flowcell362_lane4_pair1_ACAGTG"
# fname = "flowcell362_lane4_pair1_ACTTGA" # fname = "flowcell362_lane4_pair1_ACTTGA"
# fname = "flowcell362_lane4_pair1_CAGATC" # fname = "flowcell362_lane4_pair1_CAGATC"
# fname = "flowcell362_lane4_pair1_TGACCA" # fname = "flowcell362_lane4_pair1_TGACCA"
# fname = "flowcell362_lane4_pair1_Undetermined" # fname = "flowcell362_lane4_pair1_Undetermined"
# fname = "flowcell384_lane7_pair1_ACAGTG" # fname = "flowcell384_lane7_pair1_ACAGTG"
# fname = "flowcell384_lane7_pair1_ACTTGA" # fname = "flowcell384_lane7_pair1_ACTTGA"
# fname = "flowcell384_lane7_pair1_CAGATC" # fname = "flowcell384_lane7_pair1_CAGATC"
# fname = "flowcell384_lane7_pair1_GATCAG" # fname = "flowcell384_lane7_pair1_GATCAG"
# fname = "flowcell384_lane7_pair1_TGACCA" # fname = "flowcell384_lane7_pair1_TGACCA"
fname = "testing" fname = "testing"
# Print available files in 0-Raws/ directory # Print available files in 0-Raws/ directory
print("\nAvailable files :\n") print("\nAvailable files :\n")
for file in sorted(listdir("0-Raws/")): for file in sorted(listdir("0-Raws/")):
print(" - "+file.split('.')[0]) print(" - "+file.split('.')[0])
``` ```
%% Output %% Output
Available files : Available files :
- Undetermined_lane7_pair1 - Undetermined_lane7_pair1
- flowcell261_lane8_pair1_CAGATC - flowcell261_lane8_pair1_CAGATC
- flowcell261_lane8_pair1_TGACCA - flowcell261_lane8_pair1_TGACCA
- flowcell362_lane4_pair1_ACAGTG - flowcell362_lane4_pair1_ACAGTG
- flowcell362_lane4_pair1_ACTTGA - flowcell362_lane4_pair1_ACTTGA
- flowcell362_lane4_pair1_CAGATC - flowcell362_lane4_pair1_CAGATC
- flowcell362_lane4_pair1_TGACCA - flowcell362_lane4_pair1_TGACCA
- flowcell362_lane4_pair1_Undetermined - flowcell362_lane4_pair1_Undetermined
- flowcell384_lane7_pair1_ACAGTG - flowcell384_lane7_pair1_ACAGTG
- flowcell384_lane7_pair1_ACTTGA - flowcell384_lane7_pair1_ACTTGA
- flowcell384_lane7_pair1_CAGATC - flowcell384_lane7_pair1_CAGATC
- flowcell384_lane7_pair1_GATCAG - flowcell384_lane7_pair1_GATCAG
- flowcell384_lane7_pair1_TGACCA - flowcell384_lane7_pair1_TGACCA
- testing - testing
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
from pprint import pprint from pprint import pprint
fn = {n.split('.')[0] for n in listdir("0-Raws/")} fn = {n.split('.')[0] for n in listdir("0-Raws/")}
wn = {n.split('.')[0] for n in listdir("7-WIGs/")} wn = {n.split('.')[0] for n in listdir("7-WIGs/")}
lst = (n+" \t\t Processsed" if n in wn else n for n in sorted(fn)) lst = (n+" \t\t Processsed" if n in wn else n for n in sorted(fn))
[print(l) for l in lst] print("\nProcessed : {0}\n".format(len(fn & wn)))
for l in lst:
print(l)
``` ```
%% Output %% Output
Processed : 5
Undetermined_lane7_pair1 Undetermined_lane7_pair1
flowcell261_lane8_pair1_CAGATC Processsed flowcell261_lane8_pair1_CAGATC Processsed
flowcell261_lane8_pair1_TGACCA Processsed flowcell261_lane8_pair1_TGACCA Processsed
flowcell362_lane4_pair1_ACAGTG Processsed flowcell362_lane4_pair1_ACAGTG Processsed
flowcell362_lane4_pair1_ACTTGA Processsed flowcell362_lane4_pair1_ACTTGA Processsed
flowcell362_lane4_pair1_CAGATC Processsed flowcell362_lane4_pair1_CAGATC Processsed
flowcell362_lane4_pair1_TGACCA flowcell362_lane4_pair1_TGACCA
flowcell362_lane4_pair1_Undetermined flowcell362_lane4_pair1_Undetermined
flowcell384_lane7_pair1_ACAGTG flowcell384_lane7_pair1_ACAGTG
flowcell384_lane7_pair1_ACTTGA flowcell384_lane7_pair1_ACTTGA
flowcell384_lane7_pair1_CAGATC flowcell384_lane7_pair1_CAGATC
flowcell384_lane7_pair1_GATCAG flowcell384_lane7_pair1_GATCAG
flowcell384_lane7_pair1_TGACCA flowcell384_lane7_pair1_TGACCA
testing testing
[None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None]
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
%%bash %%bash
export name="testing" export name="testing"
echo $name echo $name
wc -l 3-Filtered/testing.fastq wc -l 3-Filtered/testing.fastq
wc -l 4-Bowtied/testing.sam wc -l 4-Bowtied/testing.sam
wc -l 5-ncRNA-Removed/testing.fastq wc -l 5-ncRNA-Removed/testing.fastq
``` ```
%% Output %% Output
testing testing
4000 3-Filtered/testing.fastq 4000 3-Filtered/testing.fastq
1415 4-Bowtied/testing.sam 1415 4-Bowtied/testing.sam
1780 5-ncRNA-Removed/testing.fastq 1780 5-ncRNA-Removed/testing.fastq
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
lines_to_burn = 415 lines_to_burn = 415
from time import sleep from time import sleep
with open("3-Filtered/" +fname+".fastq","r") as filtered, \ with open("3-Filtered/" +fname+".fastq","r") as filtered, \
open("4-Bowtied/" +fname+".sam","r") as matches, \ open("4-Bowtied/" +fname+".sam","r") as matches, \
open("5-ncRNA-Removed/"+fname+".fastq","w") as substracted: open("5-ncRNA-Removed/"+fname+".fastq","w") as substracted:
# Iterator over fastq file # Iterator over fastq file
filt_iter = [rec for rec in SeqIO.parse(filtered,"fastq")] filt_iter = [rec for rec in SeqIO.parse(filtered,"fastq")]
matches_iter = [l for l in matches][lines_to_burn:] matches_iter = [l for l in matches][lines_to_burn:]
for _ in range(415): matches.readline() for _ in range(415): matches.readline()
# Check last lines # Check last lines
i = 0 i = 0
im = 0 im = 0
j = 0 j = 0
jm = 0 jm = 0
ma = 0 ma = 0
pas = True pas = True
for f in filt_iter: for f in filt_iter:
i += 1 i += 1
#print() #print()
for m in matches_iter: for m in matches_iter:
m = m.split('\t')[0] m = m.split('\t')[0]
mf = m.split('\t')[9] mf = m.split('\t')[9]
if(m==f.id): if(m==f.id):
if mf==4 if mf==4
ma += 1 ma += 1
im += 1 im += 1
#print("{0}\t{1}".format(f.id,m)) #print("{0}\t{1}".format(f.id,m))
print(i) print(i)
for m in matches_iter: for m in matches_iter:
j += 1 j += 1
m = m.split('\t')[0] m = m.split('\t')[0]
for f in filt_iter: for f in filt_iter:
if(m==f.id): if(m==f.id):
jm += 1 jm += 1
#print("{0}\t{1}".format(f.id,m)) #print("{0}\t{1}".format(f.id,m))
print(i,im,j,jm) print(i,im,j,jm)
# Generator over fastq where the corresponding sam field is 4, # Generator over fastq where the corresponding sam field is 4,
# meaning no reported alignment # meaning no reported alignment
# sub_iter = (rec for rec in filt_iter \ # sub_iter = (rec for rec in filt_iter \
# if matches.readline().split('\t')[1] == '4') # if matches.readline().split('\t')[1] == '4')
# Write back fastq # Write back fastq
# SeqIO.write(sub_iter,substracted,"fastq") # SeqIO.write(sub_iter,substracted,"fastq")
``` ```
%% Output %% Output
1000 1000
1000 1000 1000 1000 1000 1000 1000 1000
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
with open("3-Filtered/" +"testing"+".fastq","r") as filtered, \ with open("3-Filtered/" +"testing"+".fastq","r") as filtered, \
open("4-Bowtied/" +"testing"+".sam","r") as matches, \ open("4-Bowtied/" +"testing"+".sam","r") as matches, \
open("5-ncRNA-Removed/"+"testing"+".fastq","w") as substracted: open("5-ncRNA-Removed/"+"testing"+".fastq","w") as substracted:
# Iterator over fastq file # Iterator over fastq file
filt_iter = SeqIO.parse(filtered,"fastq") filt_iter = SeqIO.parse(filtered,"fastq")
# Strip header (as in original script) # Strip header (as in original script)
for _ in range(415-3): matches.readline() for _ in range(415-3): matches.readline()
# Check last lines # Check last lines
print(matches.readline()) print(matches.readline())
print(matches.readline()) print(matches.readline())
print(matches.readline()) print(matches.readline())
# Generator over fastq where the corresponding sam field is 4, # Generator over fastq where the corresponding sam field is 4,
# meaning no reported alignment # meaning no reported alignment
sub_iter = (rec for rec in filt_iter \ sub_iter = (rec for rec in filt_iter \
if matches.readline().split('\t')[1] == '4') if matches.readline().split('\t')[1] == '4')
# Write back fastq # Write back fastq
SeqIO.write(sub_iter,substracted,"fastq") SeqIO.write(sub_iter,substracted,"fastq")
``` ```
%% Output %% Output
@SQ SN:tW(UCA)Q LN:74 @SQ SN:tW(UCA)Q LN:74
@SQ SN:tY(GUA)Q LN:84 @SQ SN:tY(GUA)Q LN:84
@PG ID:Bowtie VN:1.1.2 CL:"bowtie --wrapper basic-0 -S -v 3 -p 4 --best ref/2-Indexes/Yeast-Noncoding/Yeast-Noncoding 3-Filtered/testing.fastq 4-Bowtied/testing.sam" @PG ID:Bowtie VN:1.1.2 CL:"bowtie --wrapper basic-0 -S -v 3 -p 4 --best ref/2-Indexes/Yeast-Noncoding/Yeast-Noncoding 3-Filtered/testing.fastq 4-Bowtied/testing.sam"
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
%%bash %%bash
mkdir -p test/ mkdir -p test/
``` ```
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