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khalid
CroCoTest
Commits
18430303
Commit
18430303
authored
May 18, 2018
by
psimion
Browse files
various minor changes
parents
7f2d7bd3
bd02a2aa
Changes
6
Show whitespace changes
Inline
Side-by-side
src/CroCo_v1.1.sh
View file @
18430303
...
...
@@ -55,7 +55,6 @@ START_TIME=$SECONDS
if
[
$RECAT
==
"no"
]
;
then
### setting sample names
<<<<<<
< HEAD
if
[
-f
$CONFFILE
]
;
then
declare
-A
fasta_array
...
...
@@ -94,7 +93,6 @@ echo "${orders[@]}"
echo
###
=======
# i=0
#for fasta in $INDIR/*.fasta ; do
# fasta_array[$i]=`basename $fasta .fasta`
...
...
@@ -124,7 +122,6 @@ do
#for i in "${InfosCtg[@]}"; do echo $i; done;
done
<
$CONFFILE
>>>>>>>
d595607cd6e1098d1b1a5075ed876f52e30e8f4c
### detecting suspect transcripts with BLAST
#source "$my_dir/detect_suspect_trans_with_blast.sh"
...
...
@@ -148,10 +145,7 @@ done < $CONFFILE
echo
-e
"
\n
Index built :
$out
/
$toolidx
\n
"
#for (( j=0; j <i; j++ ))
<<<<<<
< HEAD
=======
#for ref in "${!fasta_array[@]}"
>>>>>>>
d595607cd6e1098d1b1a5075ed876f52e30e8f4c
for
ref
in
"
${
orders
[@]
}
"
do
refseqs
=
$out
/
$ref
".ctgs"
...
...
@@ -171,10 +165,7 @@ done < $CONFFILE
# mapping successively every read sets on all transcripts.
#for (( k=0; k <i; k++ ))
<<<<<<
< HEAD
=======
#for ref in "${!fasta_array[@]}"
>>>>>>>
d595607cd6e1098d1b1a5075ed876f52e30e8f4c
for
ref
in
"
${
orders
[@]
}
"
do
InfosCtg
=
${
fasta_array
[
$ref
]
}
...
...
@@ -256,10 +247,7 @@ done < $CONFFILE
# splitting "All_transcript.all" file into files corresponding to samples
#for (( j=0; j <i; j++ ))
<<<<<<
< HEAD
=======
#for ref in "${!fasta_array[@]}"
>>>>>>>
d595607cd6e1098d1b1a5075ed876f52e30e8f4c
for
ref
in
"
${
orders
[@]
}
"
do
#ref=${fasta_array[$j]}
...
...
src/CroCo_v1.2.sh
View file @
18430303
...
...
@@ -131,7 +131,7 @@ echo
done
# regroup all samples
refseqALL
=
$out
/ALL_transcripts.ctgs
cat
$out
/.ctgs
>
$refseqALL
cat
$out
/
$ref
.ctgs
>
$refseqALL
# mapping successively every read sets on all transcripts.
#for (( k=0; k <i; k++ ))
...
...
src/def_values.sh
View file @
18430303
...
...
@@ -15,3 +15,4 @@ SUSPID=95 # blast minimum id% for being a potential suspect of cross contamina
SUSPLEN
=
40
# blast minimum id% for being a potential suspect of cross contamination
OVEREXP
=
300
# expression level (TPM) above which a transcript might be considered "overexpressed"
RECAT
=
no
# previous CroCo output directory to be used to re-categorize transcripts
CLEANING
=
no
# cleaning reads from fastq files if they correspond to cross contaminant transcripts
src/def_values.sh~
View file @
18430303
...
...
@@ -15,3 +15,4 @@ SUSPID=95 # blast minimum id% for being a potential suspect of cross contamina
SUSPLEN=40 # blast minimum id% for being a potential suspect of cross contamination
OVEREXP=300 # expression level (TPM) above which a transcript might be considered "overexpressed"
RECAT=no # previous CroCo output directory to be used to re-categorize transcripts
CLEANING=no # cleaning reads from fastq files if they correspond to cross contaminant transcripts
src/detect_suspect_trans_with_blast.sh
View file @
18430303
...
...
@@ -42,7 +42,12 @@ done
# regroup all samples
cat
$out
/
*
.fasta_mod
>
$out
/ALL_transcripts.fasta
cat
$out
/
*
.suspects
>
$out
/ALL_transcripts.suspects
cat
$out
/
*
.fasta_suspect
>
$out
/ALL_transcripts.fasta_suspects
echo
''
>
$out
/ALL_transcripts.fasta
echo
''
>
$out
/ALL_transcripts.suspects
echo
''
>
$out
/ALL_transcripts.fasta_suspects
for
ref
in
"
${
orders
[@]
}
"
;
do
cat
$out
/
$ref
.fasta_mod
>>
$out
/ALL_transcripts.fasta
cat
$out
/
$ref
.suspects
>>
$out
/ALL_transcripts.suspects
cat
$out
/
$ref
.fasta_suspect
>>
$out
/ALL_transcripts.fasta_suspects
done
src/detect_suspect_trans_with_blast.sh~
View file @
18430303
...
...
@@ -42,7 +42,12 @@ done
# regroup all samples
cat $out/*.fasta_mod
> $out/ALL_transcripts.fasta
cat $out/*.suspects
> $out/ALL_transcripts.suspects
cat $out/*.fasta_suspect
> $out/ALL_transcripts.fasta_suspects
echo ''
> $out/ALL_transcripts.fasta
echo ''
> $out/ALL_transcripts.suspects
echo ''
> $out/ALL_transcripts.fasta_suspects
for ref in "${orders[@]}"; do
cat $out/$ref.fasta_mod >> $out/ALL_transcripts.fasta
cat $out/$ref.suspects >> $out/ALL_transcripts.suspects
cat $out/$ref.fasta_suspect >> $out/ALL_transcripts.fasta_suspects
done
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