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khalid
CroCoTest
Commits
7f2d7bd3
Commit
7f2d7bd3
authored
May 17, 2018
by
psimion
Browse files
various small changes: trying to make conf.file work
parent
e3d7f3bd
Changes
6
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src/CroCo_v1.2.sh
View file @
7f2d7bd3
...
...
@@ -131,7 +131,7 @@ echo
done
# regroup all samples
refseqALL
=
$out
/ALL_transcripts.ctgs
cat
$out
/
*
.ctgs
>
$refseqALL
cat
$out
/.ctgs
>
$refseqALL
# mapping successively every read sets on all transcripts.
#for (( k=0; k <i; k++ ))
...
...
@@ -382,6 +382,14 @@ source "$my_dir/output_network_LINKS_simplified_files.sh"
#echo -e "\tNODES_gephi_absolute.csv\n\tNODES_gephi_norm.csv\n\tNODES_diagrammer.tsv\n\tNODES_gephi_dubious_absolute.csv\n\tNODES_gephi_dubious_norm.csv\n\tNODES_diagrammer_dubious.tsv"
source
"
$my_dir
/output_network_NODES_files.sh"
### CLEANING READS
if
[
$CLEANING
==
"yes"
]
;
then
echo
-e
"
\n
Cleaning fastq files (reads mapping onto contaminant transcripts will be removed)"
source
"
$my_dir
/output_cleaned_read_files.sh"
elif
[
$CLEANING
==
"no"
]
;
then
echo
-e
"
\n
No reads cleaning will be done (parameter value set to 'no')"
fi
### miscellaneous
mkdir
network_info
mv
LINKS_
*
NODES_
*
nodes_detailed
*
.csv network_info
...
...
src/CroCo_v1.2.sh~
View file @
7f2d7bd3
...
...
@@ -131,7 +131,7 @@ echo
done
# regroup all samples
refseqALL
=
$out
/ALL_transcripts.ctgs
cat
$out
/
*
.ctgs
>
$refseqALL
cat
$out
/
$ref
.ctgs
>
$refseqALL
# mapping successively every read sets on all transcripts.
#for (( k=0; k <i; k++ ))
...
...
@@ -382,6 +382,14 @@ source "$my_dir/output_network_LINKS_simplified_files.sh"
#echo -e "\tNODES_gephi_absolute.csv\n\tNODES_gephi_norm.csv\n\tNODES_diagrammer.tsv\n\tNODES_gephi_dubious_absolute.csv\n\tNODES_gephi_dubious_norm.csv\n\tNODES_diagrammer_dubious.tsv"
source
"
$my_dir
/output_network_NODES_files.sh"
### CLEANING READS
if
[
$CLEANING
==
"yes"
]
;
then
echo
-e
"
\n
Cleaning fastq files (reads mapping onto contaminant transcripts will be removed)"
source
"
$my_dir
/output_cleaned_read_files.sh"
elif
[
$CLEANING
==
"no"
]
;
then
echo
-e
"
\n
No reads cleaning will be done (parameter value set to 'no')"
fi
### miscellaneous
mkdir
network_info
mv
LINKS_
*
NODES_
*
nodes_detailed
*
.csv network_info
...
...
src/output_cleaned_read_files.sh
0 → 100644
View file @
7f2d7bd3
### Cleaning reads if they map onto contaminant transcripts
src/output_cleaned_read_files.sh~
0 → 100644
View file @
7f2d7bd3
### Cleaning reads if they map onto contaminant transcripts
src/output_fasta.sh
View file @
7f2d7bd3
...
...
@@ -4,8 +4,10 @@ if [ $OUTPUTLEVEL == "1" ]; then
elif
[
$OUTPUTLEVEL
==
"2"
]
;
then
echo
-e
"
\n
Writing categorized transcriptomes - all categories (it might take some time)"
for
fasta
in
$out
/
*
.fasta_mod
;
do
ref
=
`
basename
$fasta
.fasta_mod
`
#for fasta in $out/*.fasta_mod; do
#ref=`basename $fasta .fasta_mod`
for
ref
in
"
${
orders
[@]
}
"
fasta
=
$out
/
$ref
".fasta_mod"
echo
-e
"
\t
$ref
"
# version awk
...
...
src/output_fasta.sh~
View file @
7f2d7bd3
...
...
@@ -4,8 +4,10 @@ if [ $OUTPUTLEVEL == "1" ]; then
elif [ $OUTPUTLEVEL == "2" ]; then
echo -e "\nWriting categorized transcriptomes - all categories (it might take some time)"
for fasta in $out/*.fasta_mod; do
ref=`basename $fasta .fasta_mod`
#for fasta in $out/*.fasta_mod; do
#ref=`basename $fasta .fasta_mod`
for ref in "${orders[@]}"
fasta=$out/$ref".fasta_mod"
echo -e "\t$ref"
# version awk
...
...
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